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4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.11 Accno Renaming File
4.11
Accno Renaming File
Scenario 1: Mapping a transcript to a gene name and adding an optional description.
Example of when this would be used: When there is no annotation file but the reference file contains gene identifiers (gene=geneName) in the header line.
YAL001C TFC3 "Largest of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauB domain of TFIIIC that binds DNA at the BoxB promoter sites of tRNA and similar genes; cooperates with Tfc6p in DNA binding"
Explanation: YAL001C is the transcript name. TFC3 is the gene name. The quoted text is the description (in this case used for both the transcript and the gene).
Scenario 2: Adding a transcript level description.
Example of when this would be used: When there is no annotation file or the annotation file does not contain a description for one or more transcripts.
YAL011W YAL011W "Protein of unknown function, component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; required for formation of nuclear-associated array of smooth endoplasmic reticulum known as karmellae"
Explanation: YAL011W is the transcript name. The quoted text is the transcript description. In this case we do not want or need to map the transcript name to a gene name.
Scenario 3: Adding a gene level description.
Example of when this would be used: When there is no annotation file or the annotation file does not contain a description for one or more genes.
CYS3 CYS3 "Cystathionine gamma-lyase, catalyzes one of the two reactions involved in the transsulfuration pathway that yields cysteine from homocysteine with the intermediary formation of cystathionine"
Explanation: CYS3 is the gene name. The quoted text is the gene description. In this case we do not want or need to rename the gene.
Scenario 4: Renaming a gene.
Example of when this would be used: A cDNA Assembly is the reference and there is external data available to map isogroup names to genes.
isogroup00001 geneName geneDescription (optional)
Explanation: isogroup00001 is the reference transcript name. geneName is the name of a gene that has been determined to correspond to the reference transcript. The geneDescription is optional.